According to AMBER Tutorial B0 ,I first run minimization for my system, then heating MD and finally production MD (npt ,then nvt).
only run minimization and heating MD with sander.MPI existing "System must be very inhomogeneous" errors, and the end of the production MD can be normal.
>>> I am clear what do you mean by "can be normal"?
Another question: the end of all steps can be normal if run MD simulation with pmemd.MPI.
I am clear what do you mean by "can be normal"?
Error information are as following:
>***** Processor 7
>***** System must be very inhomogeneous.
>***** Readjusting recip sizes.
> In this slab, Atoms found: 580 Allocated: 531
>
>
>***** Processor 9
>***** System must be very inhomogeneous.
>***** Readjusting recip sizes.
> In this slab, Atoms found: 540 Allocated: 531
>
>
>***** Processor 7
>***** System must be very inhomogeneous.
>***** Readjusting recip sizes.
> In this slab, Atoms found: 532 Allocated: 531
My input files are:
For run minization:
Initial minimisation(MM)
&cntrl
imin=1, maxcyc=16000, ncyc=4000,
ntf=1, ntc=1,
cut=8.0, ntb=2, ntp=1
/
For heat MD :
Heat 100 ps MD temp:0-300(MM)
&cntrl
imin=0,ntx=1,irest=0,
ntf=2, ntc=2, ntp=0,
cut=8.0, ntb=1,
tempi=0.0, temp0=300,
nstlim=100000, dt=0.001 ,
ntpr=1000, ntwx=1000,ntwr = 1000,
ntt=3,gamma_ln=2.0,
nmropt=1,ig=-1
/
&wttype='TEMP0',istep1=0,istep2=85000,value1=0.0,value2=300 /
&wttype='TEMP0',istep1=85001,istep2=100000,value1=300,value2=300 / &wt type='END' /
I guess there are regions of vacuum in your system.
Have you looked at your density equilibration outfile??
Maybe it could give you some hints
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: 杨满意 [mailto:ymy0664.163.com]
Sent: Monday, March 06, 2017 4:24 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Amber 16 MD simulation Problems
Dear Elvis Martis
Thanks for your reply !
MY problem is :
According to AMBER Tutorial B0 ,I first run minimization for my system, then heating MD and finally production MD (npt ,then nvt).
only run minimization and heating MD with sander.MPI existing "System must be very inhomogeneous" errors, and the end of the production MD can be normal.
>>> I am clear what do you mean by "can be normal"?
Another question: the end of all steps can be normal if run MD simulation with pmemd.MPI.
I am clear what do you mean by "can be normal"?
Error information are as following:
>***** Processor 7
>***** System must be very inhomogeneous.
>***** Readjusting recip sizes.
> In this slab, Atoms found: 580 Allocated: 531
>
>
>***** Processor 9
>***** System must be very inhomogeneous.
>***** Readjusting recip sizes.
> In this slab, Atoms found: 540 Allocated: 531
>
>
>***** Processor 7
>***** System must be very inhomogeneous.
>***** Readjusting recip sizes.
> In this slab, Atoms found: 532 Allocated: 531
My input files are:
For run minization:
Initial minimisation(MM)
&cntrl
imin=1, maxcyc=16000, ncyc=4000,
ntf=1, ntc=1,
cut=8.0, ntb=2, ntp=1
/
For heat MD :
Heat 100 ps MD temp:0-300(MM)
&cntrl
imin=0,ntx=1,irest=0,
ntf=2, ntc=2, ntp=0,
cut=8.0, ntb=1,
tempi=0.0, temp0=300,
nstlim=100000, dt=0.001 ,
ntpr=1000, ntwx=1000,ntwr = 1000,
ntt=3,gamma_ln=2.0,
nmropt=1,ig=-1
/
&wttype='TEMP0',istep1=0,istep2=85000,value1=0.0,value2=300 /
&wttype='TEMP0',istep1=85001,istep2=100000,value1=300,value2=300 / &wt type='END' /
At 2017-03-05 18:28:54, "Elvis Martis" <elvis.martis.bcp.edu.in> wrote:
>HI,
>Does your simulation crash?? Can you tell us little more about your system?
>There are similar posts on this
>http://archive.ambermd.org/201108/0444.html
>http://archive.ambermd.org/201209/0040.html
>
> Best Regards
>
>
>
>Elvis Martis
>Ph.D. Student (Computational Chemistry) at Bombay College of Pharmacy
>
>
>A Kalina, Santacruz [E], Mumbai 400098, INDIA W www.elvismartis.in
>Skype. adrian_elvis12
>
>
>
>
>-----Original Message-----
>From: 杨满意 [mailto:ymy0664.163.com]
>Sent: Sunday, March 05, 2017 9:41 AM
>To: amber.ambermd.org
>Subject: [AMBER] Amber 16 MD simulation Problems
>
>Hi,
> when I us amber 16 to do simulation, I always have the following
>probems
>
>
>***** Processor 7
>***** System must be very inhomogeneous.
>***** Readjusting recip sizes.
> In this slab, Atoms found: 580 Allocated: 531
>
>
>***** Processor 9
>***** System must be very inhomogeneous.
>***** Readjusting recip sizes.
> In this slab, Atoms found: 540 Allocated: 531
>
>
>***** Processor 7
>***** System must be very inhomogeneous.
>***** Readjusting recip sizes.
> In this slab, Atoms found: 532 Allocated: 531
>
>
>
>
>My inputfile:
> Heat 100 ps MD temp:0-300(MM)
> &cntrl
> imin=0,ntx=1,irest=0,
> ntf=2, ntc=2, ntp=0,
> cut=8.0, ntb=1,
> tempi=0.0, temp0=300,
> nstlim=100000, dt=0.001 ,
> ntpr=1000, ntwx=1000,ntwr = 1000,
> ntt=3,gamma_ln=2.0,
> nmropt=1,ig=-1
> /
>&wttype='TEMP0',istep1=0,istep2=85000,value1=0.0,value2=300 /
>&wttype='TEMP0',istep1=85001,istep2=100000,value1=300,value2=300 / &wt
>type='END' /
>
>
>
>
>How can I solve these problems. Thanks!
>
>
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Received on Mon Mar 06 2017 - 03:30:02 PST
